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Crystal structure of UBA5 fragment fused to the N-terminus of UFC1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2% (v/v) Tacsimate pH 7.0, 20% PEG 3350, 0.1M HEPES pH 7.5, 6mM zinc sulfate
Crystal Properties Matthews coefficient Solvent content 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.63 α = 90 b = 84.63 β = 90 c = 60.77 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL DECTRIS PILATUS3 6M 2019-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9763 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.65 46.78 100 0.112 0.99 13.1 20.4 7314 127.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.78 100 0.6 0.292 21.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 2Z6O 2.651 46.78 7296 373 99.986 0.219 0.2165 0.2165 0.2638 0.264 Random selection 157.069
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.318 -1.159 -2.318 7.519
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 39.925 r_dihedral_angle_2_deg 32.881 r_scangle_it 30.946 r_mcangle_it 30.387 r_scbond_it 23.011 r_mcbond_it 22.255 r_dihedral_angle_3_deg 21.976 r_dihedral_angle_4_deg 15.222 r_dihedral_angle_1_deg 7.844 r_angle_refined_deg 1.454
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 39.925 r_dihedral_angle_2_deg 32.881 r_scangle_it 30.946 r_mcangle_it 30.387 r_scbond_it 23.011 r_mcbond_it 22.255 r_dihedral_angle_3_deg 21.976 r_dihedral_angle_4_deg 15.222 r_dihedral_angle_1_deg 7.844 r_angle_refined_deg 1.454 r_nbtor_refined 0.327 r_symmetry_xyhbond_nbd_refined 0.293 r_nbd_refined 0.268 r_symmetry_nbd_refined 0.22 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.109 r_gen_planes_refined 0.006 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1488 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing